{"id":"https://openalex.org/W4360605848","doi":"https://doi.org/10.1109/isscc42615.2023.10067532","title":"A Fully Integrated End-to-End Genome Analysis Accelerator for Next-Generation Sequencing","display_name":"A Fully Integrated End-to-End Genome Analysis Accelerator for Next-Generation Sequencing","publication_year":2023,"publication_date":"2023-02-19","ids":{"openalex":"https://openalex.org/W4360605848","doi":"https://doi.org/10.1109/isscc42615.2023.10067532"},"language":"en","primary_location":{"id":"doi:10.1109/isscc42615.2023.10067532","is_oa":false,"landing_page_url":"https://doi.org/10.1109/isscc42615.2023.10067532","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2023 IEEE International Solid- State Circuits Conference (ISSCC)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5006232460","display_name":"Yen\u2010Lung Chen","orcid":"https://orcid.org/0000-0003-1580-9139"},"institutions":[{"id":"https://openalex.org/I16733864","display_name":"National Taiwan University","ror":"https://ror.org/05bqach95","country_code":"TW","type":"education","lineage":["https://openalex.org/I16733864"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Yen-Lung Chen","raw_affiliation_strings":["National Taiwan University,Taipei,Taiwan","National Taiwan University, Taipei, Taiwan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Taiwan University,Taipei,Taiwan","institution_ids":["https://openalex.org/I16733864"]},{"raw_affiliation_string":"National Taiwan University, Taipei, Taiwan","institution_ids":["https://openalex.org/I16733864"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089174139","display_name":"Chung-Hsuan Yang","orcid":"https://orcid.org/0009-0002-5239-3451"},"institutions":[{"id":"https://openalex.org/I16733864","display_name":"National Taiwan University","ror":"https://ror.org/05bqach95","country_code":"TW","type":"education","lineage":["https://openalex.org/I16733864"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Chung-Hsuan Yang","raw_affiliation_strings":["National Taiwan University,Taipei,Taiwan","National Taiwan University, Taipei, Taiwan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Taiwan University,Taipei,Taiwan","institution_ids":["https://openalex.org/I16733864"]},{"raw_affiliation_string":"National Taiwan University, Taipei, Taiwan","institution_ids":["https://openalex.org/I16733864"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015284227","display_name":"Yi-Chung Wu","orcid":"https://orcid.org/0000-0002-8774-623X"},"institutions":[{"id":"https://openalex.org/I16733864","display_name":"National Taiwan University","ror":"https://ror.org/05bqach95","country_code":"TW","type":"education","lineage":["https://openalex.org/I16733864"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Yi-Chung Wu","raw_affiliation_strings":["National Taiwan University,Taipei,Taiwan","National Taiwan University, Taipei, Taiwan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Taiwan University,Taipei,Taiwan","institution_ids":["https://openalex.org/I16733864"]},{"raw_affiliation_string":"National Taiwan University, Taipei, Taiwan","institution_ids":["https://openalex.org/I16733864"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045171042","display_name":"Chao-Hsi Lee","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Chao-Hsi Lee","raw_affiliation_strings":["GeneASIC Technologies,Hsinchu,Taiwan","GeneASIC Technologies, Hsinchu, Taiwan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"GeneASIC Technologies,Hsinchu,Taiwan","institution_ids":[]},{"raw_affiliation_string":"GeneASIC Technologies, Hsinchu, Taiwan","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041041981","display_name":"Wen-Ching Chen","orcid":null},"institutions":[{"id":"https://openalex.org/I4210120917","display_name":"Taiwan Semiconductor Manufacturing Company (Taiwan)","ror":"https://ror.org/02wx79d08","country_code":"TW","type":"company","lineage":["https://openalex.org/I4210120917"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Wen-Ching Chen","raw_affiliation_strings":["Taiwan Semiconductor Research Institute,Hsinchu,Taiwan","Taiwan Semiconductor Research Institute, Hsinchu, Taiwan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Taiwan Semiconductor Research Institute,Hsinchu,Taiwan","institution_ids":["https://openalex.org/I4210120917"]},{"raw_affiliation_string":"Taiwan Semiconductor Research Institute, Hsinchu, Taiwan","institution_ids":["https://openalex.org/I4210120917"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041221935","display_name":"Liang-Yi Lin","orcid":null},"institutions":[{"id":"https://openalex.org/I4210120917","display_name":"Taiwan Semiconductor Manufacturing Company (Taiwan)","ror":"https://ror.org/02wx79d08","country_code":"TW","type":"company","lineage":["https://openalex.org/I4210120917"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Liang-Yi Lin","raw_affiliation_strings":["Taiwan Semiconductor Research Institute,Hsinchu,Taiwan","Taiwan Semiconductor Research Institute, Hsinchu, Taiwan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Taiwan Semiconductor Research Institute,Hsinchu,Taiwan","institution_ids":["https://openalex.org/I4210120917"]},{"raw_affiliation_string":"Taiwan Semiconductor Research Institute, Hsinchu, Taiwan","institution_ids":["https://openalex.org/I4210120917"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022084541","display_name":"Nian-Shyang Chang","orcid":null},"institutions":[{"id":"https://openalex.org/I4210120917","display_name":"Taiwan Semiconductor Manufacturing Company (Taiwan)","ror":"https://ror.org/02wx79d08","country_code":"TW","type":"company","lineage":["https://openalex.org/I4210120917"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Nian-Shyang Chang","raw_affiliation_strings":["Taiwan Semiconductor Research Institute,Hsinchu,Taiwan","Taiwan Semiconductor Research Institute, Hsinchu, Taiwan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Taiwan Semiconductor Research Institute,Hsinchu,Taiwan","institution_ids":["https://openalex.org/I4210120917"]},{"raw_affiliation_string":"Taiwan Semiconductor Research Institute, Hsinchu, Taiwan","institution_ids":["https://openalex.org/I4210120917"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100744093","display_name":"Chun\u2010Pin Lin","orcid":"https://orcid.org/0000-0002-3498-1113"},"institutions":[{"id":"https://openalex.org/I4210120917","display_name":"Taiwan Semiconductor Manufacturing Company (Taiwan)","ror":"https://ror.org/02wx79d08","country_code":"TW","type":"company","lineage":["https://openalex.org/I4210120917"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Chun-Pin Lin","raw_affiliation_strings":["Taiwan Semiconductor Research Institute,Hsinchu,Taiwan","Taiwan Semiconductor Research Institute, Hsinchu, Taiwan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Taiwan Semiconductor Research Institute,Hsinchu,Taiwan","institution_ids":["https://openalex.org/I4210120917"]},{"raw_affiliation_string":"Taiwan Semiconductor Research Institute, Hsinchu, Taiwan","institution_ids":["https://openalex.org/I4210120917"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080379943","display_name":"Chi\u2010Shi Chen","orcid":null},"institutions":[{"id":"https://openalex.org/I4210120917","display_name":"Taiwan Semiconductor Manufacturing Company (Taiwan)","ror":"https://ror.org/02wx79d08","country_code":"TW","type":"company","lineage":["https://openalex.org/I4210120917"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Chi-Shi Chen","raw_affiliation_strings":["Taiwan Semiconductor Research Institute,Hsinchu,Taiwan","Taiwan Semiconductor Research Institute, Hsinchu, Taiwan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Taiwan Semiconductor Research Institute,Hsinchu,Taiwan","institution_ids":["https://openalex.org/I4210120917"]},{"raw_affiliation_string":"Taiwan Semiconductor Research Institute, Hsinchu, Taiwan","institution_ids":["https://openalex.org/I4210120917"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025474727","display_name":"Jui\u2010Hung Hung","orcid":"https://orcid.org/0000-0003-2208-9213"},"institutions":[{"id":"https://openalex.org/I148366613","display_name":"National Yang Ming Chiao Tung University","ror":"https://ror.org/00se2k293","country_code":"TW","type":"education","lineage":["https://openalex.org/I148366613"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Jui-Hung Hung","raw_affiliation_strings":["GeneASIC Technologies,Hsinchu,Taiwan","National Yang Ming Chiao Tung University, Hsinchu, Taiwan","GeneASIC Technologies, Hsinchu, Taiwan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"GeneASIC Technologies,Hsinchu,Taiwan","institution_ids":[]},{"raw_affiliation_string":"National Yang Ming Chiao Tung University, Hsinchu, Taiwan","institution_ids":["https://openalex.org/I148366613"]},{"raw_affiliation_string":"GeneASIC Technologies, Hsinchu, Taiwan","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101750729","display_name":"Chia\u2010Hsiang Yang","orcid":"https://orcid.org/0000-0003-1163-321X"},"institutions":[{"id":"https://openalex.org/I16733864","display_name":"National Taiwan University","ror":"https://ror.org/05bqach95","country_code":"TW","type":"education","lineage":["https://openalex.org/I16733864"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Chia-Hsiang Yang","raw_affiliation_strings":["National Taiwan University,Taipei,Taiwan","National Taiwan University, Taipei, Taiwan","GeneASIC Technologies, Hsinchu, Taiwan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Taiwan University,Taipei,Taiwan","institution_ids":["https://openalex.org/I16733864"]},{"raw_affiliation_string":"National Taiwan University, Taipei, Taiwan","institution_ids":["https://openalex.org/I16733864"]},{"raw_affiliation_string":"GeneASIC Technologies, Hsinchu, Taiwan","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":11,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.428,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.65307545,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":97},"biblio":{"volume":null,"issue":null,"first_page":"44","last_page":"46"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9986000061035156,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9986000061035156,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9750999808311462,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11642","display_name":"Genomics and Rare Diseases","score":0.9624000191688538,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.727432906627655},{"id":"https://openalex.org/keywords/bottleneck","display_name":"Bottleneck","score":0.7146673202514648},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6931754946708679},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.6852449178695679},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.5303500294685364},{"id":"https://openalex.org/keywords/sequence-analysis","display_name":"Sequence analysis","score":0.46027183532714844},{"id":"https://openalex.org/keywords/reference-genome","display_name":"Reference genome","score":0.44076448678970337},{"id":"https://openalex.org/keywords/genotyping","display_name":"Genotyping","score":0.43093180656433105},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.41624921560287476},{"id":"https://openalex.org/keywords/file-format","display_name":"File format","score":0.4115392565727234},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4082548916339874},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.19972214102745056},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.19568461179733276},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.19232666492462158},{"id":"https://openalex.org/keywords/embedded-system","display_name":"Embedded system","score":0.14936140179634094},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1432863473892212},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.12462359666824341}],"concepts":[{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.727432906627655},{"id":"https://openalex.org/C2780513914","wikidata":"https://www.wikidata.org/wiki/Q18210350","display_name":"Bottleneck","level":2,"score":0.7146673202514648},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6931754946708679},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.6852449178695679},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.5303500294685364},{"id":"https://openalex.org/C61053724","wikidata":"https://www.wikidata.org/wiki/Q1154615","display_name":"Sequence analysis","level":3,"score":0.46027183532714844},{"id":"https://openalex.org/C192953774","wikidata":"https://www.wikidata.org/wiki/Q7307127","display_name":"Reference genome","level":4,"score":0.44076448678970337},{"id":"https://openalex.org/C31467283","wikidata":"https://www.wikidata.org/wiki/Q912147","display_name":"Genotyping","level":4,"score":0.43093180656433105},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.41624921560287476},{"id":"https://openalex.org/C97250363","wikidata":"https://www.wikidata.org/wiki/Q235557","display_name":"File format","level":2,"score":0.4115392565727234},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4082548916339874},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.19972214102745056},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.19568461179733276},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.19232666492462158},{"id":"https://openalex.org/C149635348","wikidata":"https://www.wikidata.org/wiki/Q193040","display_name":"Embedded system","level":1,"score":0.14936140179634094},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1432863473892212},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.12462359666824341},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/isscc42615.2023.10067532","is_oa":false,"landing_page_url":"https://doi.org/10.1109/isscc42615.2023.10067532","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2023 IEEE International Solid- State Circuits Conference (ISSCC)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":5,"referenced_works":["https://openalex.org/W2593693565","https://openalex.org/W2919665556","https://openalex.org/W3014080287","https://openalex.org/W3015825547","https://openalex.org/W3101579057"],"related_works":["https://openalex.org/W2601563728","https://openalex.org/W2911891532","https://openalex.org/W1538804143","https://openalex.org/W4229588674","https://openalex.org/W4294281692","https://openalex.org/W4240057378","https://openalex.org/W4210860572","https://openalex.org/W2116114258","https://openalex.org/W2412346567","https://openalex.org/W2431161166"],"abstract_inverted_index":{"Next-generation":[0],"sequencing":[1],"(NGS)":[2],"has":[3,11,97],"revolutionized":[4],"biological":[5],"sciences":[6],"and":[7,24,46,96,141],"clinical":[8],"practices.":[9],"It":[10],"become":[12,98],"an":[13,31,34],"essential":[14],"technology":[15],"for":[16,68,85,118],"various":[17],"emerging":[18],"applications,":[19],"such":[20],"as":[21,65],"cancer":[22],"screening":[23],"inherited":[25],"disease":[26],"diagnosis.":[27],"Fig.":[28],"2.4.1":[29],"shows":[30],"overview":[32],"of":[33,56,75,114,116,162],"NGS":[35,38,104],"pipeline.":[36],"An":[37],"pipeline":[39,105],"includes":[40,132],"sample":[41],"preparation,":[42],"sequencing,":[43],"data":[44,69,77,90,129,199],"analysis":[45,78,91,130,144,189,200,206,220],"tertiary":[47,87],"analysis.":[48,70,88],"A":[49,127],"sequencer":[50],"first":[51,159],"generates":[52],"a":[53,120,196],"massive":[54],"amount":[55],"DNA":[57,121],"segments":[58],"(short-reads)":[59],"from":[60,112],"samples.":[61],"Short-reads":[62],"are":[63],"used":[64],"the":[66,76,99,102,151,158,163,167,176,187,204,219],"inputs":[67],"The":[71,89,107],"outputs":[72],"(genetic":[73],"variants)":[74],"can":[79],"then":[80],"be":[81],"sent":[82],"to":[83,149,217],"facilities":[84],"further":[86],"is":[92,171,180,191,215],"very":[93],"time":[94,153],"consuming":[95],"bottleneck":[100],"in":[101,182],"entire":[103],"[1].":[106],"high":[108],"computational":[109],"complexity":[110],"comes":[111],"hundreds":[113],"millions":[115],"short-reads":[117,211],"reconstructing":[119],"sequence":[122],"with":[123,209,213],"three":[124,160],"billion":[125],"nucleotides.":[126],"complete":[128,205],"workflow":[131],"four":[133],"steps:":[134],"short-read":[135,178],"mapping,":[136],"haplotype":[137],"calling,":[138],"variant":[139],"calling":[140],"genotyping.":[142],"Data":[143],"accelerators":[145],"have":[146],"been":[147],"proposed":[148],"reduce":[150],"processing":[152],"[2]":[154],"[3].":[155],"They":[156],"support":[157],"steps":[161],"workflow,":[164],"but":[165],"genotyping,":[166],"dominant":[168],"step":[169],"[4],":[170],"not":[172],"supported.":[173],"Additionally,":[174],"only":[175],"single-end-based":[177],"mapping":[179],"adopted":[181],"previous":[183],"works":[184],"so":[185],"that":[186,202],"achieved":[188],"accuracy":[190],"limited.":[192],"This":[193],"work":[194],"presents":[195],"fully":[197],"integrated":[198],"accelerator":[201],"handles":[203],"workflow.":[207],"Mapping":[208],"paired-end":[210],"along":[212],"rescue":[214],"utilized":[216],"enhance":[218],"accuracy.":[221]},"counts_by_year":[{"year":2025,"cited_by_count":3}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}